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- PDB-4igr: Crystal structure of the kainate receptor GluK3 ligand-binding do... -

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Basic information

Entry
Database: PDB / ID: 4igr
TitleCrystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist ZA302
ComponentsGlutamate receptor, ionotropic kainate 3
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / kainate receptor / ligand-binding domain / agonist
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / monoatomic ion transmembrane transport / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / glutamatergic synapse / dendrite / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3ZA / : / PHOSPHATE ION / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLarsen, A.P. / Venskutonyte, R. / Gajhede, M. / Kastrup, J.S. / Frydenvang, K.
Citation
Journal: J.Med.Chem. / Year: 2013
Title: Chemoenzymatic synthesis of new 2,4-syn-functionalized (S)-glutamate analogues and structure-activity relationship studies at ionotropic glutamate receptors and excitatory amino acid transporters.
Authors: Assaf, Z. / Larsen, A.P. / Venskutonyte, R. / Han, L. / Abrahamsen, B. / Nielsen, B. / Gajhede, M. / Kastrup, J.S. / Jensen, A.A. / Pickering, D.S. / Frydenvang, K. / Gefflaut, T. / Bunch, L.
#1: Journal: J.Struct.Biol. / Year: 2011
Title: Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate.
Authors: Venskutonyte, R. / Frydenvang, K. / Gajhede, M. / Bunch, L. / Pickering, D.S. / Kastrup, J.S.
History
DepositionDec 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5496
Polymers29,0921
Non-polymers4575
Water91951
1
A: Glutamate receptor, ionotropic kainate 3
hetero molecules

A: Glutamate receptor, ionotropic kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,09912
Polymers58,1852
Non-polymers91410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2630 Å2
ΔGint-40 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.180, 68.180, 126.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-902-

K

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor, ionotropic kainate 3 / Glutamate receptor 7 / GluR-7 / GluR7


Mass: 29092.453 Da / Num. of mol.: 1
Fragment: Ligand-binding domain, UNP RESIDUES 432-546, 669-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur7, Grik3 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42264

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Non-polymers , 5 types, 56 molecules

#2: Chemical ChemComp-3ZA / (4R)-4-{3-[hydroxy(methyl)amino]-3-oxopropyl}-L-glutamic acid


Mass: 248.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N2O6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTRANSMEMBRANE REGIONS 547-668 WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (547-548)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 % / Mosaicity: 0.98 °
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→42.173 Å / Num. obs: 9062 / % possible obs: 98.7 % / Redundancy: 4.6 % / Biso Wilson estimate: 49 Å2 / Rsym value: 0.108 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.65-2.794.60.4420.391.9598713070.2010.4420.393.799.9
2.79-2.964.60.3080.2732.8572512460.140.3080.273599.9
2.96-3.174.60.210.1864534711640.0950.210.1866.699.9
3.17-3.424.60.1480.1315.5504510950.0670.1480.131999.5
3.42-3.754.60.1140.101745639920.0520.1140.10111.298.9
3.75-4.194.60.0920.0817.841499050.0410.0920.08113.498.5
4.19-4.844.60.0930.0827.737438120.0420.0930.08215.197.9
4.84-5.934.60.1040.0926.230906750.0470.1040.09214.196.6
5.93-8.384.50.0790.078.324405430.0360.0790.0713.595.3
8.38-42.1733.90.0620.0549.812703230.0290.0620.05416.292.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S9E

3s9e


Resolution: 2.65→35.866 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8185 / SU ML: 0.39 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 432 4.78 %RANDOM
Rwork0.198 ---
obs0.2014 9029 97.9 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.896 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 127.66 Å2 / Biso mean: 49.3494 Å2 / Biso min: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.3157 Å2-0 Å2-0 Å2
2---0.3157 Å2-0 Å2
3---0.6314 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 25 51 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172088
X-RAY DIFFRACTIONf_angle_d1.1662799
X-RAY DIFFRACTIONf_chiral_restr0.074309
X-RAY DIFFRACTIONf_plane_restr0.004352
X-RAY DIFFRACTIONf_dihedral_angle_d16.342779
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.65-3.03330.32471560.2551282429802824100
3.0333-3.8210.27531380.203128552993285599
3.821-35.86960.2391380.17429183056291895
Refinement TLS params.Method: refined / Origin x: -6.5402 Å / Origin y: 31.3615 Å / Origin z: -14.7263 Å
111213212223313233
T0.2434 Å20.0497 Å2-0.0879 Å2-0.147 Å2-0.0223 Å2--0.1632 Å2
L1.1898 °2-0.0969 °20.5804 °2-1.953 °20.4606 °2--1.3176 °2
S0.1872 Å °0.0952 Å °-0.2864 Å °0.1318 Å °0.0678 Å °-0.2386 Å °0.4269 Å °0.1808 Å °0.0598 Å °
Refinement TLS groupSelection details: ALL

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